BACKGROUND: The COVID-19 pandemic represents a complex challenge for medical staff within emergency departments (ED) of hospitals at all care levels. Beside regular emergency care, rapid detection and isolation of COVID-19 cases are obligatory for prevention of internal viral transmission and efficient medical staff protection. METHODS: In this study a model of risk stratification for suspected SARS-CoV­2 and COVID-19 cases was developed on the basis of epidemiologic criteria of the Robert-Koch Institute including five risk categories (RC). The model was implemented in a hospital of basic and regular care level. By combination of risk categories with specific isolation, hygienic and personal protection procedures all areas of the ED were restructured. In a retrospective study all inpatient cases (n = 491) were re-evaluated during a 4-week interval (26 March-26 April 2020). RESULTS: In the study population 25 SARS-CoV­2 positive cases (5.2%) were identified. These cases were categorized according to the risk stratification model as follows: RC I-confirmed SARS-CoV­2 infection 36% (n = 9), RC II-reasonable suspected cases 32% (n = 8), RC III-differential diagnostic cases 12% (n = 3), RC IV-low probability 8% (n = 2) and RC V-no evidence 12% (n = 3). No viral transmission was detected during the whole period within medical staff and patients of the ED. CONCLUSIONS: Introduction of COVID-19 risk categories within the ED permits central control of important hygienic processes with respect to SARS-CoV­2 infection probability. By continuous re-evaluation of case definitions local outbreaks can be used to adapt criteria within the risk categories. Risk stratification of COVID-19 cases allows for a strict separation of COVID-19 and non-COVID-19 emergencies and thus ensures effective infection prevention of medical staff and patients.